Hello all!

I'm trying to analyze 16 Affy arrays with SAM, Limma and RankProd to
look at differential expression.

I got the following error message from the RP function.  Any help as to
what it means?

> RP.out<- RP(eset_rma, eset.cl, num.perm = 100, logged=TRUE,
na.rm=FALSE, plot=FALSE, gene.names=eset.gnames)
Error in if (total.sam != total.sam2) stop("Number of classes should
match the columns in the data") : 
        argument is of length zero

I have included below the phenotype data of eset_rma and the listing of
eset.cl:

> pData(eset_rma)
                   SAMPLE_NUM TREATMENT TCELLS
NE_MDM-INF1.CEL             1       INF      N
NE_MDM-INF2.CEL             2       INF      N
NE_MDM-INF3.CEL             3       INF      N
NE_MDM-INF4.CEL             4       INF      N
NE_MDM-T-1.CEL              5    NONINF      Y
NE_MDM-T-2.CEL              6    NONINF      Y
NE_MDM-T-3.CEL              7    NONINF      Y
NE_MDM-T-4.CEL              8    NONINF      Y
NE_MDM-T-INF-1.CEL          9       INF      Y
NE_MDM-T-INF-2.CEL         10       INF      Y
NE_MDM-T-INF-3.CEL         11       INF      Y
NE_MDM-T-INF-4.CEL         12       INF      Y
NE_MDM1.CEL                13    NONINF      N
NE_MDM2.CEL                14    NONINF      N
NE_MDM3.CEL                15    NONINF      N
NE_MDM4.CEL                16    NONINF      N

> eset.cl
 [1]  1  2  3  4 -5 -6 -7 -8  5  6  7  8 -1 -2 -3 -4

Thanks for any help you can provide!

---Nick Ettinger

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